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+0000100751 00000 n +0000100856 00000 n +0000100965 00000 n +trailer +<< +/Size 15 +/Info 1 0 R +/Root 2 0 R +>> +startxref +101043 +%%EOF diff --git a/tool_conf.xml.sample b/tool_conf.xml.sample index fd7fc2069e2..2d0abaf6fd2 100644 --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -294,4 +294,10 @@ --> +
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diff --git a/tools/metag_tools/short_reads_figure_length.py b/tools/metag_tools/short_reads_figure_length.py new file mode 100644 index 00000000000..9842163984b --- /dev/null +++ b/tools/metag_tools/short_reads_figure_length.py @@ -0,0 +1,209 @@ +#! /usr/bin/python +""" +Galaxy +to commit +4.2 for i, line in enumerate(file(filename)): +4.4 stop passing read_seqfile and read_scorefile around +4.5 use --> if __name__ == "__main__": __main__() +5. use galaxy extention +Input: + sequence file(s): zip or text file --> for 454 and Solexa +Output: + pdf files from R, length histogram --> before and after trim +---- +Wen-Yu Chung +""" +import os, sys, math, tempfile, zipfile, re +from rpy import * + +# default and initialize values +number_of_points = 20 +read_seqfile = [] +read_scorefile = [] +title_keys = [] +seq_hash = {} +score_hash = {} +trim_seq_hash = {} +tmp_seq = '' +tmp_score = [] # change variables here + +length_before_trim = [] +length_after_trim = [] +score_points = [] + +database_tmp = "/tmp/" # default dir: current directory +if (not os.path.isdir(database_tmp)): + os.mkdir(database_tmp) + +# functions +def stop_err(msg): + + sys.stderr.write(msg) + sys.stderr.write("\n") + sys.exit() + + +def read_input_files(file_list): + + read_file = [] + + for file_name in file_list: + infile = open(file_name,'r') + read_file = infile.readlines() + infile.close() + + return read_file + + +def unzip_files(file_name): + + read_file = [] + + temp_dir_name = tempfile.mkdtemp() + '/' #dir=database_tmp + temp_new_dest = temp_dir_name + file_name.split('/')[-1] + command_line = 'cp ' + file_name + ' ' + temp_dir_name + '\nunzip ' + temp_new_dest + ' -d ' + temp_dir_name + + os.system(command_line) + os.remove(temp_new_dest) + + dest = os.listdir(temp_dir_name) + if ((len(dest) == 1) and (os.path.isdir(dest[0]))): + new_file_dir = temp_dir_name + dest[0] + '/' + dest = os.listdir(new_file_dir) + else: + new_file_dir = temp_dir_name + + for filex in dest: + filex = new_file_dir + filex + read_file.append(filex) + + return new_file_dir, read_file + + +def parse_solexa_files(result, type): + # parse solexa seq and probability files only + # not fasta format + # assign numeric id + + tmp_hash = {} + tmp_title = '' + tmp_seq = '' + tmp_id = 0 + + if (type == 'seq'): + for each_line in result: + tmp_seq = '' + each_line.strip('\r\n') + tmp_id += 1 + fasta_id = '>' + str(tmp_id) + (run_id, file_id, read_x, read_y, read) = each_line.split() + tmp_hash[(fasta_id)] = read + else: # type == score + for each_line in result: + tmp_seq = [] + each_line.strip('\r\n') + tmp_id += 1 + fasta_id = '>' + str(tmp_id) + each_loc = each_line.split('\t') + for each_base in each_loc: + each_nuc_error = each_base.split() + each_nuc_error[0] = int(each_nuc_error[0]) + each_nuc_error[1] = int(each_nuc_error[1]) + each_nuc_error[2] = int(each_nuc_error[2]) + each_nuc_error[3] = int(each_nuc_error[3]) + big = max(each_nuc_error) + #baseIndex = each_nuc_error.index(big) + tmp_seq.append(big) + tmp_hash[(fasta_id)] = tmp_seq + + return tmp_hash + + +def parse_fasta_format(result): + # detect whether it's score or seq files + # return a hash: key = title and value = seq + + tmp_hash = {} + tmp_title = '' + tmp_seq = '' + + for each_line in result: + each_line = each_line.strip('\r\n') + if (each_line[0] == '>'): + if (len(tmp_seq) > 0): + tmp_hash[(tmp_title)] = tmp_seq + tmp_title = each_line + tmp_seq = '' + else: + tmp_seq = tmp_seq + each_line + if (each_line.split()[0].isdigit()): + tmp_seq = tmp_seq + ' ' + if (len(tmp_seq) > 0): + tmp_hash[(tmp_title)] = tmp_seq + + return tmp_hash + + +def generate_hist_figure(): + # R module and code + + tmp_array = [] + + # data for R hist + # write the length only! + outfile = open(outfile_R_name,'w') + title_keys = seq_hash.keys() + for read_title in title_keys: + tmp_seq = seq_hash[(read_title)] + length_before_trim.append(len(tmp_seq)) + print >> outfile, len(tmp_seq) + outfile.close() + + max_length_before_trim = max(length_before_trim) + + # generate pdf figures + """ + outfile_R_pdf = outfile_R_name + r.pdf(outfile_R_pdf) + + title = infile_seq_name.split('/')[-1] + xlim_range = [1,max_length_before_trim] + r.hist(length_before_trim,prob=1, xlab="Read length (bp)", ylab="Frequency (%)", xlim=xlim_range, main=title, nclass=100) + r.dev_off() + """ + return 0 + + +# I/O +infile_seq_name = sys.argv[1].strip() +outfile_R_name = sys.argv[2].strip() + +# to unzip or not unzip file +tmp_seq_dir = '' +seq_file_list = [] +if (zipfile.is_zipfile(infile_seq_name)): (tmp_seq_dir, seq_file_list) = unzip_files(infile_seq_name) +else: seq_file_list = [infile_seq_name] +read_seqfile = read_input_files(seq_file_list) +if (os.path.isdir(tmp_seq_dir)): + for file_name in seq_file_list: + os.remove(file_name) + os.removedirs(tmp_seq_dir) + +# detect whether it's tabular or fasta format +if read_seqfile[0].startswith(">"): + seq_method = '454' +else: + seq_method = 'solexa' + + +# parse files +if (seq_method == 'solexa'): + seq_hash = parse_solexa_files(read_seqfile, 'seq') +else: # the other two are both fasta format + seq_hash = parse_fasta_format(read_seqfile) + +# R +status = generate_hist_figure() + +# close and remove temporary files +r.quit(save = "no") diff --git a/tools/metag_tools/short_reads_figure_length.xml b/tools/metag_tools/short_reads_figure_length.xml new file mode 100644 index 00000000000..c77e4866fbf --- /dev/null +++ b/tools/metag_tools/short_reads_figure_length.xml @@ -0,0 +1,44 @@ + +on sequence file + +short_reads_figure_length.py $input1 $output1 + + + + + + + + + + + + + + + + + + + + + + + + +.. class:: infomark + +For **Sanger**, **454 or Solexa** sequencing technology only. + +----- + +**What it does** + +This tool takes a multi-fasta sequence file and outputs a text file: + +- an array of the lengths in the file + +To see the distribution, please use the Histogram tool in Graph/Display data. + + + diff --git a/tools/metag_tools/short_reads_figure_score.py b/tools/metag_tools/short_reads_figure_score.py new file mode 100644 index 00000000000..4bb62fb8df1 --- /dev/null +++ b/tools/metag_tools/short_reads_figure_score.py @@ -0,0 +1,266 @@ +#! /usr/bin/python +""" +Galaxy +to commit +4.2 for i, line in enumerate(file(filename)): +4.4 stop passing read_seqfile and read_scorefile around +4.5 use --> if __name__ == "__main__": __main__() +5. use galaxy extention +Input: + quality score file(s): zip or text file +Output: +pdf files from R + score distribution --> boxplot, Solexa as 36bp, 454 as 20 points +---- +Wen-Yu Chung +""" +import os, sys, math, tempfile, zipfile, re +from rpy import * + +# default and initialize values +number_of_points = 20 +read_seqfile = [] +read_scorefile = [] +title_keys = [] +seq_hash = {} +score_hash = {} +trim_seq_hash = {} +tmp_seq = '' +tmp_score = [] # change variables here + +length_before_trim = [] +length_after_trim = [] +score_points = [] + +database_tmp = "/tmp/" # default dir: current directory +if (not os.path.isdir(database_tmp)): + os.mkdir(database_tmp) + +# functions +def stop_err(msg): + + sys.stderr.write(msg) + sys.stderr.write("\n") + sys.exit() + + +def read_input_files(file_list): + + read_file = [] + + for file_name in file_list: + infile = open(file_name,'r') + read_file = infile.readlines() + infile.close() + + return read_file + + +def unzip_files(file_name): + + read_file = [] + + temp_dir_name = tempfile.mkdtemp() + '/' #dir=database_tmp + temp_new_dest = temp_dir_name + file_name.split('/')[-1] + command_line = 'cp ' + file_name + ' ' + temp_dir_name + '\nunzip ' + temp_new_dest + ' -d ' + temp_dir_name + + os.system(command_line) + os.remove(temp_new_dest) + + dest = os.listdir(temp_dir_name) + if ((len(dest) == 1) and (os.path.isdir(dest[0]))): + new_file_dir = temp_dir_name + dest[0] + '/' + dest = os.listdir(new_file_dir) + else: + new_file_dir = temp_dir_name + + for filex in dest: + filex = new_file_dir + filex + read_file.append(filex) + + return new_file_dir, read_file + + +def parse_solexa_files(result, type): + # parse solexa seq and probability files only + # not fasta format + # assign numeric id + + tmp_hash = {} + tmp_title = '' + tmp_seq = '' + tmp_id = 0 + + if (type == 'seq'): + for each_line in result: + tmp_seq = '' + each_line.strip('\r\n') + tmp_id += 1 + fasta_id = '>' + str(tmp_id) + (run_id, file_id, read_x, read_y, read) = each_line.split() + tmp_hash[(fasta_id)] = read + else: # type == score + for each_line in result: + tmp_seq = [] + each_line.strip('\r\n') + tmp_id += 1 + fasta_id = '>' + str(tmp_id) + each_loc = each_line.split('\t') + for each_base in each_loc: + each_nuc_error = each_base.split() + each_nuc_error[0] = int(each_nuc_error[0]) + each_nuc_error[1] = int(each_nuc_error[1]) + each_nuc_error[2] = int(each_nuc_error[2]) + each_nuc_error[3] = int(each_nuc_error[3]) + big = max(each_nuc_error) + #baseIndex = each_nuc_error.index(big) + tmp_seq.append(big) + tmp_hash[(fasta_id)] = tmp_seq + + return tmp_hash + + +def parse_fasta_format(result): + # detect whether it's score or seq files + # return a hash: key = title and value = seq + + tmp_hash = {} + tmp_title = '' + tmp_seq = '' + + for each_line in result: + each_line = each_line.strip('\r\n') + if (each_line[0] == '>'): + if (len(tmp_seq) > 0): + tmp_hash[(tmp_title)] = tmp_seq + tmp_title = each_line + tmp_seq = '' + else: + tmp_seq = tmp_seq + each_line + if (each_line.split()[0].isdigit()): + tmp_seq = tmp_seq + ' ' + if (len(tmp_seq) > 0): + tmp_hash[(tmp_title)] = tmp_seq + + return tmp_hash + + +def generate_boxplot_figure(): + # R module and code + + score_matrix = [] + tmp_array = [] + + # data for R boxplot + title_keys = score_hash.keys() + if (seq_method == 'solexa'): + for read_title in title_keys: + score_points.append(score_hash[(read_title)]) + else: + for read_title in title_keys: + tmp_score = '0 ' + score_hash[(read_title)] + tmp_list = tmp_score.split() + read_length = len(tmp_list) + if (read_length > 100): + step = int(math.floor((read_length-1)*1.0/number_of_points)) + score = [] + point = 1 + point_sum = 0 + step_average = 0 + for i in xrange(1,read_length): + if (i < (point * step)): + point_sum += int(tmp_list[i]) + step_average += 1 + else: + point_avg = point_sum*1.0/step_average + score.append(point_avg) + point += 1 + point_sum = 0 + step_average = 0 + + if (step_average > 0): + point_avg = point_sum*1.0/step_average + score.append(point_avg) + + if (len(score) > number_of_points): + last_avg = 0 + for j in xrange(number_of_points-1,len(score)): + last_avg += score[j] + last_avg = last_avg/(len(score)-number_of_points+1) + else: + last_avg = score[-1] + score_points_tmp = [] + for k in range(number_of_points-1): + score_points_tmp.append(score[k]) + score_points_tmp.append(last_avg) + score_points.append(score_points_tmp) + score_points_tmp = [] + + # reverse the matrix, for R + for i in range(number_of_points-1): + for j in range(len(score_points)): + tmp_array.append(score_points[j][i]) + score_matrix.append(tmp_array) + tmp_array = [] + + # generate pdf figures + outfile_R_pdf = outfile_R_name + r.pdf(outfile_R_pdf) + + #title = infile_score_name.split('/')[-1] + title = "boxplot of quality scores" + if (seq_method=='solexa'): + r.boxplot(score_matrix,xlab="location in read length",main=title) + else: + r.boxplot(score_matrix,xlab="percentage in read length",xaxt="n",main=title) + x_old_range = [] + x_new_range = [] + step = 100/number_of_points + for i in xrange(0,100,step): + x_old_range.append((i/step)) + x_new_range.append(i) + r.axis(1,x_old_range,x_new_range) + + r.dev_off() + + return 0 + + +# I/O +infile_score_name = sys.argv[1].strip() +outfile_R_name = sys.argv[2].strip() + +# to unzip or not unzip file +tmp_score_dir = '' +score_file_list = [] +if (zipfile.is_zipfile(infile_score_name)): (tmp_score_dir, score_file_list) = unzip_files(infile_score_name) +else: score_file_list = [infile_score_name] +read_scorefile = read_input_files(score_file_list) +if (os.path.isdir(tmp_score_dir)): + for file_name in score_file_list: + os.remove(file_name) + os.removedirs(tmp_score_dir) + +# detect whether it's tabular or fasta format +if read_scorefile[0].startswith(">"): + seq_method = '454' +else: + seq_method = 'solexa' + +# detect whether it's a sequence file +if re.match('[A-Z]', read_scorefile[1]): + stop_err("this is not a quality score file.") + +# parse files +if (seq_method == 'solexa'): + score_hash = parse_solexa_files(read_scorefile, 'score') + number_of_points = 36 +else: # the other two are both fasta format + score_hash = parse_fasta_format(read_scorefile) + number_of_points = 20 + +print seq_method, number_of_points + +# R +status = generate_boxplot_figure() +r.quit(save = "no") diff --git a/tools/metag_tools/short_reads_figure_score.xml b/tools/metag_tools/short_reads_figure_score.xml new file mode 100644 index 00000000000..4084f28c73a --- /dev/null +++ b/tools/metag_tools/short_reads_figure_score.xml @@ -0,0 +1,42 @@ + +on a boxplot + +short_reads_figure_score.py $input1 $output1 + + + + + + + + + + + + + +.. class:: infomark + +For **Sanger**, **454 or Solexa** sequencing technology only. + +----- + +**What it does** + +This tool takes quality score files and outputs one file: + +- figures in pdf file showing score distribution. + + + diff --git a/tools/metag_tools/short_reads_run_phred.py b/tools/metag_tools/short_reads_run_phred.py new file mode 100644 index 00000000000..e21e8f5ff71 --- /dev/null +++ b/tools/metag_tools/short_reads_run_phred.py @@ -0,0 +1,108 @@ +#! /usr/bin/python +""" +Galaxy +to commit +2. use galaxy extention +Input: +trace file(s): zip or single scf file --> for Sanger +Output: +1. sequcence file +2. quality score file +---- +Wen-Yu Chung +""" +import os, sys, math, tempfile, zipfile, re + +# default and initialize values +number_of_points = 20 +read_seqfile = [] +read_scorefile = [] +title_keys = [] +seq_hash = {} +score_hash = {} +trim_seq_hash = {} +tmp_seq = '' +tmp_score = [] # change variables here + +length_before_trim = [] +length_after_trim = [] +score_points = [] + +database_tmp = "/tmp/" # default dir: current directory +if (not os.path.isdir(database_tmp)): + os.mkdir(database_tmp) + +# functions +def stop_err(msg): + + sys.stderr.write(msg) + sys.stderr.write("\n") + sys.exit() + + +def unzip_files(file_name): + + read_file = [] + + temp_dir_name = tempfile.mkdtemp() + '/' #dir=database_tmp + temp_new_dest = temp_dir_name + file_name.split('/')[-1] + command_line = 'cp ' + file_name + ' ' + temp_dir_name + '\nunzip ' + temp_new_dest + ' -d ' + temp_dir_name + + os.system(command_line) + os.remove(temp_new_dest) + + dest = os.listdir(temp_dir_name) + if ((len(dest) == 1) and (os.path.isdir(dest[0]))): + new_file_dir = temp_dir_name + dest[0] + '/' + dest = os.listdir(new_file_dir) + else: + new_file_dir = temp_dir_name + + for filex in dest: + filex = new_file_dir + filex + read_file.append(filex) + + return new_file_dir, read_file + + +def parse_trace_files(infile_name): + + trace_file = [] + tmp_dir = '' + seq_file_name = tempfile.mkstemp()[1] #tempfile.NamedTemporaryFile(dir=database_tmp).name + score_file_name = tempfile.mkstemp()[1] #tempfile.NamedTemporaryFile(dir=database_tmp).name + file_list_name = tempfile.mkstemp()[1] #tempfile.NamedTemporaryFile(dir=database_tmp).name + file_list = open(file_list_name,'w') + + if (zipfile.is_zipfile(infile_name)): + (tmp_dir, trace_file) = unzip_files(infile_name) + else: + trace_file = [infile_name] + for i in trace_file: + print >> file_list,i + file_list.close() + + # call phred + phred_command = '~/phred/phred -if ' + file_list_name + ' -sa ' + seq_file_name + ' -qa ' + score_file_name + ' -process_nomatch 2>/dev/null' + os.system(phred_command) + + # remove every scf file and the file_list itself + if (os.path.isdir(tmp_dir)): + for i in trace_file: + os.remove(i) + os.removedirs(tmp_dir) + os.remove(file_list_name) + + return seq_file_name, score_file_name + +def __main__(): + # I/O + infile_name = sys.argv[1].strip() + outfile_seq_name = sys.argv[2].strip() + outfile_score_name = sys.argv[3].strip() + + (infile_seq_name, infile_score_name)=parse_trace_files(infile_name) + os.system("mv " + infile_seq_name + " " + outfile_seq_name) + os.system("mv " + infile_score_name + " " + outfile_score_name) + +if __name__ == "__main__" : __main__() diff --git a/tools/metag_tools/short_reads_run_phred.xml b/tools/metag_tools/short_reads_run_phred.xml new file mode 100644 index 00000000000..10bae28dba6 --- /dev/null +++ b/tools/metag_tools/short_reads_run_phred.xml @@ -0,0 +1,27 @@ + + return sequence and score files + short_reads_run_phred.py $input1 $output1 $output2 + + + + + + + + +.. class:: infomark + +For **trace (abi and scf) file** only. + +----- + +**What it does** + +This tool takes raw data from sequencing facility and outputs two files: + +- sequences in fasta format; + +- quality score. + + + diff --git a/tools/metag_tools/short_reads_trim_seq.py b/tools/metag_tools/short_reads_trim_seq.py new file mode 100644 index 00000000000..71c92e95569 --- /dev/null +++ b/tools/metag_tools/short_reads_trim_seq.py @@ -0,0 +1,329 @@ +#! /usr/bin/python +""" +Galaxy +to commit +1. filter: select read length longer than a threshold without trimming (minimum score = 0?) +4. incorporate greg's changes. +4.2 for i, line in enumerate(file(filename)): +4.4 stop passing read_seqfile and read_scorefile around +4.5 use --> if __name__ == "__main__": __main__() +5. use galaxy extention +6. a better trimming process for 454 (homopolymers) +6.1 to keep the longest homoloplymers +Input: +1. sequence file(s): zip or text file --> for 454 and Solexa +2. quality score file(s): zip or text file --> for 454 and Solexa +3. trace file(s): zip or single scf file --> for Sanger +4. threshold to trim the sequence +5. threshold of the trimmed sequence length to be reported +Output: +trimmed sequence in one file +---- +Wen-Yu Chung +""" +import os, sys, math, tempfile, zipfile, re +#from rpy import * + +# default and initialize values +number_of_points = 20 +read_seqfile = [] +read_scorefile = [] +title_keys = [] +seq_hash = {} +score_hash = {} +trim_seq_hash = {} +tmp_seq = '' +tmp_score = [] # change variables here + +length_before_trim = [] +length_after_trim = [] +score_points = [] + +database_tmp = "/tmp/" # default dir: current directory +if (not os.path.isdir(database_tmp)): + os.mkdir(database_tmp) + +# functions +def stop_err(msg): + + sys.stderr.write(msg) + sys.stderr.write("\n") + sys.exit() + + +def read_input_files(file_list): + + read_file = [] + + for file_name in file_list: + infile = open(file_name,'r') + read_file = infile.readlines() + infile.close() + + return read_file + + +def unzip_files(file_name): + + read_file = [] + + temp_dir_name = tempfile.mkdtemp() + '/' #dir=database_tmp + temp_new_dest = temp_dir_name + file_name.split('/')[-1] + command_line = 'cp ' + file_name + ' ' + temp_dir_name + '\nunzip ' + temp_new_dest + ' -d ' + temp_dir_name + + os.system(command_line) + os.remove(temp_new_dest) + + dest = os.listdir(temp_dir_name) + if ((len(dest) == 1) and (os.path.isdir(dest[0]))): + new_file_dir = temp_dir_name + dest[0] + '/' + dest = os.listdir(new_file_dir) + else: + new_file_dir = temp_dir_name + + for filex in dest: + filex = new_file_dir + filex + read_file.append(filex) + + return new_file_dir, read_file + + +def parse_solexa_files(result, type): + # parse solexa seq and probability files only + # not fasta format + # assign numeric id + + tmp_hash = {} + tmp_title = '' + tmp_seq = '' + tmp_id = 0 + + if (type == 'seq'): + for each_line in result: + tmp_seq = '' + each_line.strip('\r\n') + tmp_id += 1 + fasta_id = '>' + str(tmp_id) + #(run_id, file_id, read_x, read_y, read) = each_line.split() + tmp_values = each_line.split() + read = tmp_values[-1] + tmp_hash[(fasta_id)] = read + else: # type == score + for each_line in result: + tmp_seq = [] + each_line.strip('\r\n') + tmp_id += 1 + fasta_id = '>' + str(tmp_id) + each_loc = each_line.split('\t') + for each_base in each_loc: + each_nuc_error = each_base.split() + each_nuc_error[0] = int(each_nuc_error[0]) + each_nuc_error[1] = int(each_nuc_error[1]) + each_nuc_error[2] = int(each_nuc_error[2]) + each_nuc_error[3] = int(each_nuc_error[3]) + big = max(each_nuc_error) + #baseIndex = each_nuc_error.index(big) + tmp_seq.append(big) + tmp_hash[(fasta_id)] = tmp_seq + + return tmp_hash + + +def parse_fasta_format(result): + # detect whether it's score or seq files + # return a hash: key = title and value = seq + + tmp_hash = {} + tmp_title = '' + tmp_seq = '' + + for each_line in result: + each_line = each_line.strip('\r\n') + if (each_line[0] == '>'): + if (len(tmp_seq) > 0): + tmp_hash[(tmp_title)] = tmp_seq + tmp_title = each_line + tmp_seq = '' + else: + tmp_seq = tmp_seq + each_line + if (each_line.split()[0].isdigit()): + tmp_seq = tmp_seq + ' ' + if (len(tmp_seq) > 0): + tmp_hash[(tmp_title)] = tmp_seq + + return tmp_hash + + +def trim_seq(): + # trim sequence + title_keys = seq_hash.keys() + for read_title in title_keys: + tmp_seq = seq_hash[(read_title)] + if (seq_method == 'solexa'): + tmp_score = score_hash[(read_title)] + else: + tmp_score = score_hash[(read_title)].split() + + trim_seq = '' + + for i in range(len(tmp_seq)): + if (int(tmp_score[i]) > threshold_trim): + pass_nuc = tmp_seq[i:(i+1)] + else: + pass_nuc = ' ' + trim_seq = trim_seq + pass_nuc + + # find the max substrings + segments = trim_seq.split() + max_segment = '' + len_max_segment = 0 + + if (threshold_report == 0): + for each_segment in segments: + if (len_max_segment < len(each_segment)): + max_segment = each_segment + ',' + len_max_segment = len(each_segment) + elif (len_max_segment == len(each_segment)): + max_segment = max_segment + each_segment + ',' + else: + for each_segment in segments: + if (len(each_segment) >= threshold_report): + max_segment = max_segment + each_segment + ',' + + trim_seq_hash[(read_title)] = max_segment[0:-1] + + return trim_seq_hash + +def __main__(): + # I/O + seq_method = sys.argv[1].strip().lower() + try: + threshold_trim = int(sys.argv[2].strip()) + except: + stop_err("Invalid value for minimal quality score") + try: + threshold_report= int(sys.argv[3].strip()) + except: + stop_err("Invalid value for minimal sequence length") + outfile_seq_name = sys.argv[4].strip() + infile_seq_name = sys.argv[5].strip() + infile_score_name = sys.argv[6].strip() + + # to unzip or not unzip file + tmp_seq_dir = '' + seq_file_list = [] + if (zipfile.is_zipfile(infile_seq_name)): (tmp_seq_dir, seq_file_list) = unzip_files(infile_seq_name) + else: seq_file_list = [infile_seq_name] + read_seqfile = read_input_files(seq_file_list) + if (os.path.isdir(tmp_seq_dir)): + for file_name in seq_file_list: + os.remove(file_name) + os.removedirs(tmp_seq_dir) + + tmp_score_dir = '' + score_file_list = [] + if (zipfile.is_zipfile(infile_score_name)): (tmp_score_dir, score_file_list) = unzip_files(infile_score_name) + else: score_file_list = [infile_score_name] + read_scorefile = read_input_files(score_file_list) + if (os.path.isdir(tmp_score_dir)): + for file_name in score_file_list: + os.remove(file_name) + os.removedirs(tmp_score_dir) + + # parse files + if (seq_method == 'solexa'): + seq_hash = parse_solexa_files(read_seqfile, 'seq') + score_hash = parse_solexa_files(read_scorefile, 'score') + if (threshold_report > 36): + print "the read length from solexa is 36bp, your choice of read length is not valid.\n" + print "the threshold is set to zero (return the longest substring).\n" + threshold_report = 0 + number_of_points = 36 + else: # the other two are both fasta format + seq_hash = parse_fasta_format(read_seqfile) + score_hash = parse_fasta_format(read_scorefile) + number_of_points = 20 + + # trim sequence + trim_seq_hash = trim_seq() + + # output trimmed sequence to a fasta file + outfile_seq = open(outfile_seq_name,'w') + title_keys = seq_hash.keys() + for read_title in title_keys: + tmp_seq = seq_hash[(read_title)] + tmp_trim_seq = trim_seq_hash[(read_title)].split(',') + if (len(tmp_trim_seq) > 1): + for i in range(len(tmp_trim_seq)): + print >> outfile_seq, "%s %d\n%s" % (read_title, i, tmp_trim_seq[i]) + elif (len(tmp_trim_seq[0]) > 0): + print >> outfile_seq, "%s\n%s" % (read_title, tmp_trim_seq[0]) + outfile_seq.close() + +#if __name__ == "__main__": __main__() +if 1: + # I/O + seq_method = sys.argv[1].strip().lower() + try: + threshold_trim = int(sys.argv[2].strip()) + except: + stop_err("Invalid value for minimal quality score") + try: + threshold_report= int(sys.argv[3].strip()) + except: + stop_err("Invalid value for minimal sequence length") + outfile_seq_name = sys.argv[4].strip() + infile_seq_name = sys.argv[5].strip() + infile_score_name = sys.argv[6].strip() + + # to unzip or not unzip file + tmp_seq_dir = '' + seq_file_list = [] + if (zipfile.is_zipfile(infile_seq_name)): (tmp_seq_dir, seq_file_list) = unzip_files(infile_seq_name) + else: seq_file_list = [infile_seq_name] + read_seqfile = read_input_files(seq_file_list) + if (os.path.isdir(tmp_seq_dir)): + for file_name in seq_file_list: + os.remove(file_name) + os.removedirs(tmp_seq_dir) + + tmp_score_dir = '' + score_file_list = [] + if (zipfile.is_zipfile(infile_score_name)): (tmp_score_dir, score_file_list) = unzip_files(infile_score_name) + else: score_file_list = [infile_score_name] + read_scorefile = read_input_files(score_file_list) + if (os.path.isdir(tmp_score_dir)): + for file_name in score_file_list: + os.remove(file_name) + os.removedirs(tmp_score_dir) + + # parse files + if (seq_method == 'solexa'): + seq_hash = parse_solexa_files(read_seqfile, 'seq') + score_hash = parse_solexa_files(read_scorefile, 'score') + if (threshold_report > 36): + print "the read length from solexa is 36bp, your choice of read length is not valid.\n" + print "the threshold is set to zero (return the longest substring).\n" + threshold_report = 0 + number_of_points = 36 + else: # the other two are both fasta format + seq_hash = parse_fasta_format(read_seqfile) + score_hash = parse_fasta_format(read_scorefile) + number_of_points = 20 + + # trim sequence + trim_seq_hash = trim_seq() + + # output trimmed sequence to a fasta file + outfile_seq = open(outfile_seq_name,'w') + title_keys = seq_hash.keys() + for read_title in title_keys: + tmp_seq = seq_hash[(read_title)] + tmp_trim_seq = trim_seq_hash[(read_title)].split(',') + if (len(tmp_trim_seq) > 1): + for i in range(len(tmp_trim_seq)): + print >> outfile_seq, "%s %d\n%s" % (read_title, i, tmp_trim_seq[i]) + elif (len(tmp_trim_seq[0]) > 0): + print >> outfile_seq, "%s\n%s" % (read_title, tmp_trim_seq[0]) + outfile_seq.close() + diff --git a/tools/metag_tools/short_reads_trim_seq.xml b/tools/metag_tools/short_reads_trim_seq.xml new file mode 100644 index 00000000000..f0d29c1591d --- /dev/null +++ b/tools/metag_tools/short_reads_trim_seq.xml @@ -0,0 +1,72 @@ + +based on quality scores + +#if $sequencing_method_choice.sequencer=="454":#short_reads_trim_seq.py 454 $trim $length $output1 $input1 $input2 +#else:#short_reads_trim_seq.py solexa $trim $length $output1 $input1 $input2 +#end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +.. class:: infomark + +For **Sanger**, **454 or Solexa** sequencing technology only. +Either trace file or both of the read file and quality score file must be provided. + +----- + +**What it does** + +This tool takes raw data from sequencing facility and outputs a multi-fasta file: + +- trimmed sequences in fasta format; + +If *minimal trimmed length to report* is set to a number larger than zero, the tool ouputs any substrings that are longer than this threshold. +If there are more than one substring, the tool outputs all of them in separated fasta format. + + +